KABT BioBlog

The 21st Century Prometheans?

A little over a year ago, Brad posted a link to a survey on Synthetic Biology.  Although it appears that little has fundamentally changed since then, this burgeoning field, along side nanotechnology, has become front page news, and will hopefully become a topic of conversation in your biology class in the near future.

I don’t pretend to be an expert on Synthetic Biology but I thought a few resources may provide you with enough background knowledge to approach the topic with your students this year.  Maybe they could use this post itself as a springboard for discussion or more research.  The post is in three parts, each accompanied by some thought provoking quotes from Mary Shelley’s Frankenstein…

Early Years and Standford’s Drew Endy

In these links you will will find a reference to one of the first papers in the field, a few comic responses to the field, and links to two YouTube videos (originally TED Talks) of Drew Endy explaining the difference between Synthetic Biology and the more standard and familiar recombinant DNA and genetic engineering technologies.

“The world was to him a secret which he desired to divine. Curiosity, earnest research to learn the hidden laws of nature, gladness akin to rapture, as they were unfolded to him, are among the earliest sensations he can remember . . . It was the secrets of heaven and earth that he desired to learn; and whether it was the outward substance of things or the inner spirit of nature and the mysterious soul of man that occupied him, still his inquiries were directed to the metaphysical, or in it highest sense, the physical secrets of the world.”

1. Synthetic Biology: Engineering Escherichia coli to see light (November 2005)
2. Nature’s comic on Synthetic Biology (November 2005)
3. The Story of Synthia - another comic look at synthetic biology
4. Synthetic Biology Organization with a press link to numerous popular critiques of synthetic biology
5. SEED’s Cribsheet on Synthetic Biology (July 2010)

(June 2007)

(December 2008)

Venter creates the News & President Obama’s Responds

“There was none among the myriads of men that existed who would pity or assist me; and should I feel kindness towards my enemies? No: from that moment I declared everlasting war against the species, and, more than all, against him who had formed me and sent me forth to this insupportable misery.”

(May 2010)

1. The President’s Emerging Technologies Interagency Policy Coordination Committee’s Inaugural Meeting (May 2010)
2. NPR Story, Presidential Panel Scrutinizes Synthetic Biology (July 2010)

Resources for those interested in Doing some Synthetic Biology

The following resources are for entering the field of Synthetic Biology.  The first link will introduce you to an annual competition used to motivate undergraduate teams of students to design and engineer novel pathways in E. coli.  If you search around, I think that you’ll find that there has been a single high school team involved in the competition before.  Some of university sponsors are quite interested in developing a kit to introduce students to the methods synthetic biology.

1. iGEM 2010
2. Authentic Teaching and Learning through Synthetic Biology based the E. coli engineered to sense light
3. The BioBricks Foundation
4. Registry of Standard Biological Parts
5. BioBrick Assembly Kit from New England BioLabs

“‘The labours of men of genius, however erroneously directed, scarcely ever fail in ultimately turning to the solid advantage of mankind.”

Observations at a Volleyball Court, accompanied by an ID & Behavioral Challenge

While on holiday in Oklahoma this weekend, I happened by this volleyball court on the way to the pool.   My attention was immediately drawn to movements that I observed in my periphery.  Here is what I observed from sand level…

and close-up from above…

The species may be territorial.  While individuals came close to each other it appeared like there were brief chases and overall there was an emergent spatial pattern (I think you can see it in the first video) suggestive of territoriality.   I tried to follow the movement of a single individual but it was too difficult for me.

After spending more time, continuing to ignore my children swimming and doing flips of the side of the pool, I made these more detailed observations suggestive of territoriality as well.  In the first video, you will see interactions between numerous live individuals with a single dead individual of the same species…

Here is a close-up image of an instance of this behavior…

In the second video, you will see interactions of these hymenoptera with a mottled leaf…

Here is a close-up image of an instance of this behavior…

The fact that the colors of the leaf are similar to some of those found in the wasps themselves made me wonder if I could elicit the behavior with another leaf.  The leaf I chose to use, unlike the one I found them naturally interacting with, was entirely yellow.  What do you hypothesize will happen?

Around the periphery of the volleyball court, I noticed holes in the sand that were approximately the same diameter as the cylinder shape of the insect themselves (see below), although maybe a bit weathered.  I should have dug them up but didn’t think of it at the time.

I had noticed similar behavior in a much smaller number of cicada killers in a children’s sandbox, but had no idea what type of hymenoptera this species was.  Similar, I wondered, was this a mating swarm?  Where they recently emerged individuals?  What was the ratio of genders?  How long does this behavior persist?  What resources might they use to maintain their energy?

A few curious individuals did happen to come by while I was making my observations, and I received seemingly conflicting reports on their longevity.  One adult mentioned that they are there all the time, while a couple of kids arriving to play volleyball hadn’t noticed them there the day before.  In fact, later that night I saw, from afar, four people playing volleyball.  I might add, that to get some of the images and video, I walked in amongst the swarm.  I did so slowly but felt that they may have ignored me even if I had walked in at a normal pace.

So, here’s the challenge…

• What is the genus and/or species of this hymenoptera?  and
• What the heck are they doing?

As mentioned in response to Brad’s post on aphids, I think a collection of such videos and images could make an interesting series of ecological activities for students, and possibly a series of models for them to produce their own reports, blogs, etc… on interesting outdoor observations that can motivate learning of particular ecological principles.

For anyone that responds with the answers, unknown to me with any certainty, it would be nice, and potentially helpful in the future, for you to provide links to websites that helped in your identification.

A number of years ago, I developed a method for teaching students about the basic structure of the cell membrane that has proven to be both enjoyable and memorable, and after receiving positive feedback upon sharing this activity with my friends at the Center for BioMolecular Modeling at the Milwaukee School of Engineering, I figured that it is time that a share it with a larger community of individuals.

Simply, the method is a ”thought experiment” in which students graphically hypothesize the arrangement of a collection of molecules unknown to them (phospholipids) in three sequential situations, in order to personally discover the self-assembly of phospholipids in generating a simplified cell membrane.

Once students have discovered this basic image of a cell for themselves it becomes easier for them to supplement it generating a more complex conception of the cell.

In fact, I usually draw an analogy between the cellular container and the test tubes and beakers used in chemistry.  Student readily understand that cells, “as places where chemical reactions occur” require:

• a container (the goal of this series of thought experiments),
• reactants,
• points of entry and exit (the membrane and supplemental proteins),
• a solvent (the water inside this simple cell),
• catalysts as biological enzymes,
• energy,
• and a controlling region or some means of regulation.

A summary of the “thought experiment” follows but for those that want more details, including images, or would rather read offline, I have created a document explaining this Cell Membrane Thought Experiment.

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Observations of tadpoles in a local pond

Two days ago, while driving my eldest daughter and a friend to morning swim practice, we ran across, but not over, a rather large snapping turtle crossing the road.  This happened just east of Mission Road on 71st Street in Shawnee Misson, Kansas (it appears that he may have grown up in Indian Hills County Club).  Although the turtle appears to have lived quite a productive live to that moment, we figured that we might increase its life span by moving him somewhere a little bit less populated.

Yesterday, my two younger children and I, released our find in a wetland area adjacent to the Blue River in southern Johnson County.  While there, I treated my kids to one of the ponds I frequent with students when I am teaching about amphibians.  Here is an interesting observation that we made…

A quick google search this morning suggests that field biologist may not fully understand this behavior, and not for lack of thoughtful consideration and experimentation.  I know that school is out and that critical observations and experimentation are dependent on the life cycle of an organism who doesn’t realize that, but I share this observation none-the-less, for its potential…

…and if you want to ID the tadpoles you can do that too…

Where the Mule Deer and the Pronghorn Antelope Play…

Reflections on the KABT Field Trip in Logan County, June 4-6, 2010

I am not sure what KABT’s goal for the field trip were but for me they were two-fold.  I wanted to provide an inspirational outdoor experience for four of my senior students, and two of my children, who eagerly participated in the trip, while learning myself about the wonderful short-grass prairie from our very own sage, the Yoda-like natural history master, Stan Roth. 

In both regards the trip was a resounding success, even though I failed to continue to follow Noah’s driving lead into better pastures where he was finally able to witness the character of our pursuit, the endangered a recently re-established Black-Footed Ferret (see Noah’s posts). 

If you are sad that you missed the trip, continue on since I did my best to record it all for you…

More specifically, follow along to see what I saw, learn what I learned, listen while I contemplate what KABT may have learned, and educate yourself on the prairie dog wars of Logan County, Kansas in hopes of a return trip to this wonderful county… 

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OK. I have a lot of thoughts that I need to put down about the field trip to Logan Co., KS this last weekend. I will need some time to organize those. But for now, I will post this pic with words describing this amazing experience to soon follow.

What are those dark ones?

In last week’s  “Biology Challenge”, I challenged biology teachers to contribute identifications and descriptions of the relationships illustrated in a photo of aphids, ants and milkweeds.  Sure enough, within an hour the milkweed was successfully identified as Asclepias syrica and the aphids as Aphis nerii.  A number of various Formica species were sent in as tentative identification for the ants in the image.   Though, I would not begin to suggest I know much about ants I am pretty sure you’ll find that these ants belong to the genus Crematogaster–the acrobat ants.   Mark DuBois produced a Checklist of Kansas Ants in the Kansas School Naturalist that includes possible candidates.  There are any number of resources on the web that might lead us to an identification if I collected some of the ants.

But what I really want to get to is the nature of the interactions taking place on the tip of the milkweed leaf.  Several people noted that the ants were tending the aphids in a classic ant/aphid mutualistic relationship.  There’s several items that complicate this however and I think this image can serve as an open door to an incredible landscape of accessible student study.  For starters, while ants do tend aphids on milkweed–the aphids tend to be Aphis asclepias and not A. nerii–that’s what caught my eye.  Hmmmm…A. nerii presumably sports the bright yellows and oranges as warning coloration.  If ants don’t typically tend A. nerii then perhaps the aphid’s  “honeydew” is somehow not as toxic as normal in this instance.   Milkweed plants vary in their toxicity–perhaps parts of the individual milkweed vary in toxicity as well.

Check out Herbivory.com, Anurag Agrawal’s web site for a truly in depth introduction to the milkweed ecological community.  In particular check out his powerpoints and videos under the Multimedia tab.  These will introduce you to the incredible complexity of community level interactions that he and his colleagues are uncovering.  Specifically link to his Publications tab–there, you’ll find a very rich resource of pdf’s that will help you to see the milkweed communities in a different light and help you to guide your students inquiry.   I have spent hours reading these papers.  I think you’ll find that many of them are very accessible.  Here’s a Discover blog post that introduces one of the studies:  Mooney, K. A. and A. A. Agrawal. Plant genotype shapes ant-aphid interactions: implications for community structure and indirect plant defense. American Naturalist 171: E195–E205. Here’s another relevant paper and a link to it:    Smith, R.A., K.A. Mooney and A. A. Agrawal. Coexistence of three specialist aphids on the common milkweed Asclepias syriaca. Ecology 89: 2187–2196.

Once a person starts to focus observations on a relationship like that illustrated in the photo from my original post, then all sorts of questions come to mind.  I propose that this is one of our jobs as biology teachers–put students into a situation/an environment that promotes original and accessible student questions.  Help them to focus their observations and reconcile them with what they know and don’t know.  Questions will follow.   What does this take in the classroom?  Not much really,  start a butterfly garden,  participate in the Monarch Watch’s Waystation Program.  Participate in Monarch Larval Monitoring project.  Here’s a resource on aphid from the MLMP:  Monitoring Aphids.  Participate in the earthworm project that Eric shared.  Participation in projects like these almost invariably leads to students asking all kinds of questions.  At first they are very general and non-focused but with only a little help with some guiding questions from their instructor the students natural curiosity can be turned to powerful questions for study.

Years ago, in the process of helping to establish the Monarch Watch with Chip Taylor, I would promote Monarchs in the classroom by reminding folks of Karl Von Frisch’s description of his honeybees:

“The bee’s life is like a magic well: the more you draw from it, the more it fills with water”.

Really, any natural system is like that once you start to pay attention to detail. Natural systems exude wonder and complexity that begs study. Exploit this with your students—introduce them to doing science by “drawing from the well”….

Looking for a new outdoor ecology investigation to conduct with your students?  … something that will require them to get their hands dirty?  … and aid in their learning and appreaciation for our native fauna? 

Then look no further than the new citizens science project, Earthworms Across Kansas organized by Dr. Bruce Snyder at Kansas State University.  As stated on their website and in an introductory letter I recieved a few weeks ago…

Earthworms Across Kansas is a free program that engages middle and high school students throughout the state in answering some basic, yet unanswered questions about Kansas earthworms, such as “Which species are here?” and “What are the ranges of these species?”

The project aims to educate Kansas’ middle and high school students about earthworm biology and invasive species issues by engaging them as citizen scientists.  One-third of the approximately 170 species of earthworms known to reside in the United States have arrived here from another continent.  We expect that most every earthworm your students collect will be an exotic species.

We are currently recruiting teachers to participate (online registration form), although only until we run out of kits.  Once registered, you can prepare for your participation by viewing curricula and lesson plans associated with earthworm biology that will be posted online through May.  In July or August your kit will be mailed, and your students can complete their collecting anytime during the 2010-2011 academic year.  The data from across the state will be uploaded on their interactive google map, and thus facilitate your students answering the basic questions posed by the project.

If you’d like more information about the program before registering certainly visit their website, and if you have further questions, please email the project at earthworm@k-state.edu.

I haven’t read through the protocols for this project yet but thought you may interested in learning from the active worm collectors and the research associated with their methods.  Check out Worm Grunting, Fiddling, and Charming—Humans Unknowingly Mimic a Predator to Harvest Bait published in PLOS.  Besides the article there are a number of interesting quicktime video links demonstrating the research.

Here’s a cool but complex ecological interaction directly involving at least three species going on in my backyard. (Olathe, KS)

We’ve had a mostly cool and wet spring to date.  The plant involved is about 0.6 m tall at this point and there is a large flower bud within these leaves.  For this challenge, let’s start with the names of the species involved (at least to genus) followed by a description of the interactions involved.  Turns out there is a great site on the web that has this all documented with photos and scientific papers.  Maybe you can find that.  Part of the reason I put this challenge here is to hopefully inspire biology teachers into thinking just what they and their students might be able to investigate with just a small butterfly garden.  Another image:

btw, I’m putting this challenge up on the NABT BioBlog at the same time—I want to see who figures this out first–the KABTer’s or the NABTer’s……challenge on.

A few months ago, I spent quite a bit of time searching for science related apps that could potentially be useful for my life as a biology teacher.  I have downloaded a number and have had the opportunity to discover those that I have found most useful (or potentially useful) in that role.

The main post contains a list of 16 iPhone apps.  Each app icon is followed by a brief description and links that may be helpful for you in making a decision on acquiring the app.   For those that I have found especially useful, I discuss specific manner(s) it has been used.  Furthermore, if you don’t have an iPhone some of the producers of these apps have websites that may be useful as well.

For those unfamiliar with iPhones, these apps must be acquired through the apps store in iTunes so in many cases there are not internet links to pages with further information on these apps.  To learn more, download iTunes, and search the app names in the iTunes store, or google search and read what you can find.

Happy app hunting…

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